Xmipp

xmipp_micrograph_automatic_picking (v3.0)

Usage

Automatic particle picking for micrographs The algorithm is designed to learn the particles from the user, as well as from its own errors. The algorithm is fully described in this paper.

Parameters

-i <micrograph>
Micrograph image
--outputRoot <rootname>
Output rootname
--mode <mode>
Operation mode
where <mode> can be:
  • try Try to autoselect within the training phase.
  • train <posfile=> posfile contains the coordinates of manually picked particles _auto_feature_vectors.txt contains the particle structure created by this program when used in automatic selection mode _false_positives.xmd contains the list of false positives among the automatically picked particles
  • autoselect Autoselect
--model <model_rootname>
Bayesian model of the particles to pick
--particleSize <size>
Particle size in pixels
--thr <p=1>
Number of threads for automatic picking
--fast
Perform a fast preprocessing of the micrograph (Fourier filter instead of Wavelet filter)
--in_core
Read the micrograph in memory

Examples and notes

Automatically select particles during training:
xmipp_micrograph_automatic_picking -i micrograph.tif --particleSize 100 --model model --thr 4 --outputRoot micrograph --mode try 
Training:
xmipp_micrograph_automatic_picking -i micrograph.tif --particleSize 100 --model model --thr 4 --outputRoot micrograph --mode train manual.pos
Automatically select particles after training:
xmipp_micrograph_automatic_picking -i micrograph.tif --particleSize 100 --model model --thr 4 --outputRoot micrograph --mode autoselect

User's comments

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